Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	49855
Gene name	S-phase cyclin A associated protein in the ER
Gene symbol	SCAPER
Synonyms (NCBI Gene)	IDDRPMSTP063ZNF291Zfp291
Chromosome	15
Chromosome location	15q24.3

Show/Hide all (16)

SNP ID	Visualize variation	Clinical significance	Consequence
rs777893794	G>A	Likely-pathogenic	Stop gained, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs978336151	G>A,T	Likely-pathogenic	Non coding transcript variant, synonymous variant, coding sequence variant, stop gained
rs1239725461	G>A	Likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1303625185	GA>-	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, frameshift variant, non coding transcript variant
rs1305542291	C>T	Likely-pathogenic, pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant, non coding transcript variant
rs1395475624	CTT>-	Likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, genic upstream transcript variant, inframe deletion
rs1462082548	T>-,TT	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1484749107	G>A,C	Likely-pathogenic	Stop gained, coding sequence variant, missense variant, non coding transcript variant, 5 prime UTR variant, genic upstream transcript variant
rs1555447569	ATTG>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, frameshift variant
rs1555558169	T>C	Pathogenic	Splice acceptor variant
rs1567499068	G>-	Pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, stop gained
rs1596596355	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant, downstream transcript variant, non coding transcript variant
rs1597752941	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant, non coding transcript variant
rs1598279469	G>C	Likely-pathogenic	Intron variant
rs1598598205	C>T	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1598632432	A>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant, non coding transcript variant

Show/Hide all (4)

miRTarBase ID	miRNA	Experiments	Reference
MIRT439702	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT439702	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT1328386	hsa-miR-3671	CLIP-seq
MIRT1328387	hsa-miR-888	CLIP-seq

Show/Hide all (17)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001541	Process	Ovarian follicle development	IEA
GO:0001547	Process	Antral ovarian follicle growth	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0005515	Function	Protein binding	IPI	17698606, 32814053
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005829	Component	Cytosol	IDA
GO:0007283	Process	Spermatogenesis	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0016607	Component	Nuclear speck	IDA
GO:0046872	Function	Metal ion binding	IEA
GO:0060041	Process	Retina development in camera-type eye	IMP	28794130
GO:0061827	Component	Sperm head	IEA
GO:0072520	Process	Seminiferous tubule development	IEA
GO:1990917	Component	Ooplasm	IEA

MIM	HGNC	e!Ensembl
611611	13081	ENSG00000140386

Q9BY12

Protein name

S phase cyclin A-associated protein in the endoplasmic reticulum (S phase cyclin A-associated protein in the ER) (Zinc finger protein 291)

Protein function

CCNA2/CDK2 regulatory protein that transiently maintains CCNA2 in the cytoplasm.

PDB

8BPO

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF16501	SCAPER_N	89 → 186	S phase cyclin A-associated protein in the endoplasmic reticulum	Family
PF12874	zf-met	792 → 816		Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed with high expression in testis. Isoform 1 is detected in various tissues, including retina, fetal and adult brain. Isoform 2 is expressed in the retina at high levels, and in the brain at very low levels (PubMed:287941

Sequence

MMASFQRSNSHDKVRRIVAEEGRTARNLIAWSVPLESKDDDGKPKCQTGGKSKRTIQGTH
KTTKQSTAVDCKITSSTTGDKHFDKSPTKTRHPRKIDLRARYWAFLFDNLRRAVDEIYVT
CESDQSVVECKEVLMMLDNYVRDFKALIDWIQLQEKLEKTDAQSRPTSLAWEVKKMSPGR
HVIPSPSTDRINVTSNARRSLNFGGSTGTVPAPRLAPTGVSWADKVKAHHTGSTASSEIT
PAQSCPPMTVQKASRKNERKDAEGWETVQRGRPIRSRSTAVMPKVSLATEATRSKDDSDK
ENVCLLPDESIQKGQFVGDGTSNTIESHPKDSLHSCDHPLAEKTQFTVSTLDDVKNSGSI
RDNYVRTSEISAVHIDTECVSVMLQAGTPPLQVNEEKFPAEKARIENEMDPSDISNSMAE
VLAKKEELADRLEKANEEAIASAIAEEEQLTREIEAEENNDINIETDNDSDFSASMGSGS
VSFCGMSMDWNDVLADYEARESWRQNTSWGDIVEEEPARPPGHGIHMHEKLSSPSRKRTI
AESKKKHEEKQMKAQQLREKLREEKTLKLQKLLEREKDVRKWKEELLDQRRRMMEEKLLH
AEFKREVQLQAIVKKAQEEEAKVNEIAFINTLEAQNKRHDVLSKLKEYEQRLNELQEERQ
RRQEEKQARDEAVQERKRALEAERQARVEELLMKRKEQEARIEQQRQEKEKAREDAARER
ARDREERLAALTAAQQEAMEELQKKIQLKHDESIRRHMEQIEQRKEKAAELSSGRHANTD
YAPKLTPYERKKQCSLCNVLISSEVYLFSHVKGRKHQQAVRENTSIQGRELSDEEVEHLS
LKKYIIDIVVESTAPAEALKDGEERQKNKKKAKKIKARMNFRAKEYESLMETKNSGSDSP
YKAKLQRLAKDLLKQVQVQDSGSWANNKVSALDRTLGEITRILEKENVADQIAFQAAGGL
TALEHILQAVVPATNVNTVLRIPPKSLCNAINVYNLTCNNCSENCSDVLFSNKITFLMDL
LIHQLTVYVPDENNTILGRNTNKQVFEGLTTGLLKVSAVVLGCLIANRPDGNCQPATPKI
PTQEMKNKPSQGDPFNNRVQDLISYVVNMGLIDKLCACFLSVQGPVDENPKMAIFLQHAA
GLLHAMCTLCFAVTGRSYSIFDNNRQDPTGLTAALQATDLAGVLHMLYCVLFHGTILDPS
TASPKENYTQNTIQVAIQSLRFFNSFAALHLPAFQSIVGAEGLSLAFRHMASSLLGHCSQ
VSCESLLHEVIVCVGYFTVNHPDNQVIVQSGRHPTVLQKLCQLPFQYFSDPRLIKVLFPS
LIAACYNNHQNKIILEQEMSCVLLATFIQDLAQTPGQAENQPYQPKGKCLGSQDYLELAN
RFPQQAWEEARQFFLKKEKK

Sequence length

1400

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Attention deficit hyperactivity disorder	Pathogenic	rs1555447569	RCV000515799	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual developmental disorder and retinitis pigmentosa; IDDRP	Likely pathogenic; Pathogenic	rs761149240, rs2050148457, rs757834403, rs2151864247, rs1192028272, rs1555447569, rs1555558169, rs1305542291, rs1395475624, rs1239725461, rs1303625185, rs1596596355, rs1462082548, rs978336151, rs1598632432 View all (5 more)	RCV001783712 RCV001783713 RCV001813898 RCV002221861 RCV003989435 View all (15 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Moderate intellectual disability	Pathogenic; Likely pathogenic	rs1555447569, rs1305542291, rs1395475624	RCV000515799 RCV000523592 RCV000520792	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa	Pathogenic	rs1555558169	RCV000578475	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rod-cone dystrophy	Pathogenic; Likely pathogenic	rs1555447569, rs1305542291, rs1395475624	RCV000515799 RCV000523592 RCV000520792	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SCAPER-related disorder	Likely pathogenic	rs2050148457, rs2548144366, rs1239045609	RCV004731179 RCV003400295 RCV003397443	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Syndromic retinitis pigmentosa	Pathogenic	rs1555558169	RCV001003221	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (31)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARDET-BIEDL SYNDROME	—	Disgenet, Orphanet Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bardet-Biedl syndrome 1	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
BRACHYDACTYLY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY THROMBOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DENTAL ENAMEL HYPOPLASIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIVERTICULAR DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DEVELOPMENTAL DISORDER AND RETINITIS PIGMENTOSA	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DEVELOPMENTAL DISORDER AND RETINITIS PIGMENTOSA, IDDRP	—	ClinVar, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTRACRANIAL HEMORRHAGE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IRRITABLE BOWEL SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LATE-ONSET ALZHEIMER'S DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDER	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBSTRUCTIVE SLEEP APNEA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal dystrophy	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Uncertain significance	ClinVar Disgenet, GWAS catalog Disgenet, GWAS catalog	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SCOLIOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (45)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Age related macular degeneration	Age-related macular degeneration	BEFREE	19412524		★★★★★ ★☆☆☆☆ Found in Text Mining only
Age related macular degeneration	Age-related macular degeneration	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Attention Deficit Disorder with Hyperactivity	Attention deficit hyperactivity disorder	Pubtator	30561111	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	CLINVAR_DG	28794130		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bardet-Biedl Syndrome	Bardet-Biedl Syndrome	BEFREE	30723319		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brachydactyly	Brachydactyly	CLINVAR_DG	30723319		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cataract	Cataract	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Diverticular Diseases	Diverticular Diseases	GWASCAT_DG	30177863		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypogonadism	Hypogonadism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
INTELLECTUAL DEVELOPMENTAL DISORDER AND RETINITIS PIGMENTOSA	Intellectual Developmental Disorder And Retinitis Pigmentosa	GENOMICS_ENGLAND_DG	28041643		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DEVELOPMENTAL DISORDER AND RETINITIS PIGMENTOSA	Intellectual Developmental Disorder And Retinitis Pigmentosa	UNIPROT_DG	28794130		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DEVELOPMENTAL DISORDER AND RETINITIS PIGMENTOSA	Intellectual Developmental Disorder And Retinitis Pigmentosa	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	CTD_human_DG	21937992		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Intellectual developmental disorder	Pubtator	30561111, 37295431	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	BEFREE	30723319		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Keratoconus	Keratoconus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★★★★★ ★☆☆☆☆ Found in Text Mining only
Macular Degeneration	Macular degeneration	Pubtator	19412524	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Mental deficiency	Mental retardation	CTD_human_DG	21937992		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Moderate intellectual disability	Mental retardation	CLINVAR_DG	28794130		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neuroblastoma	Neuroblastoma	BEFREE	30723319		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nuclear cataract	Cataract	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	CLINVAR_DG	30723319		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
obsolete Peripheral retinopathy	Obsolete Peripheral Retinopathy	CLINVAR_DG	30723319		★★★★★ ★☆☆☆☆ Found in Text Mining only
obsolete Rod-cone dystrophy	Rod-cone dystrophy	CLINVAR_DG	28794130		★★★★★ ★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Profound Mental Retardation	Mental retardation	CTD_human_DG	21937992		★★★★★ ★☆☆☆☆ Found in Text Mining only
Reticulosarcoma	Reticulosarcoma	BEFREE	22890838		★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	ORPHANET_DG	28794130		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	CLINVAR_DG	28794130		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa	Retinitis Pigmentosa	Orphanet			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	30561111, 37295431	Associate	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	30723319		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
RHYNS syndrome	Rhyns syndrome	Pubtator	30561111	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Speech Disorders	Speech Disorders	CLINVAR_DG	30723319		★★★★★ ★☆☆☆☆ Found in Text Mining only

SCAPER (S-phase cyclin A associated protein in the ER)